Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis

E Hartman, AM Scott, C Karlsson, T Mohanty… - Nature …, 2023 - nature.com
The incorporation of machine learning methods into proteomics workflows improves the
identification of disease-relevant biomarkers and biological pathways. However, machine …

Unravelling potential biomarkers for acute and chronic brucellosis through proteomic and bioinformatic approaches

Y Yang, K Qiao, Y Yu, Y Zong, C Liu… - Frontiers in Cellular and …, 2023 - frontiersin.org
Introduction This study aimed to identify biomarkers for acute and chronic brucellosis using
advanced proteomic and bioinformatic methods. Methods Blood samples from individuals …

Population scale proteomics enables adaptive digital twin modelling in sepsis

AM Scott, L Mellhammar, E Malmström… - MedRxiv, 2024 - medrxiv.org
Sepsis is one of the leading causes of mortality in the world. Currently, the heterogeneity of
sepsis makes it challenging to determine the molecular mechanisms that define the …

Explainable machine learning for the identification of proteome states via the data processing kitchen sink

AM Scott, E Hartman, J Malmström, L Malmström - BioRxiv, 2023 - biorxiv.org
The application of machine learning algorithms to facilitate the understanding of changes in
proteome states has emerged as a promising methodology in proteomics research …

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment

B Wen, J Freestone, M Riffle, MJ MacCoss, WS Noble… - bioRxiv, 2024 - biorxiv.org
A pressing statistical challenge in the field of mass spectrometry proteomics is how to assess
whether a given software tool provides accurate error control. Each software tool for …

DeepBINN: A tailored biologically-informed neural network for robust biomarker identification

J Meirer, LD Wittwer, V Revol… - 2024 11th IEEE Swiss …, 2024 - ieeexplore.ieee.org
Biologically-informed neural networks (BINNs) have recently been proposed to aid in
identifying disease-relevant biomarkers and biological pathways using deep neural …